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- PDB-6td7: Structure of truncated hemoglobin THB11 from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 6td7
TitleStructure of truncated hemoglobin THB11 from Chlamydomonas reinhardtii
ComponentsTHB11
KeywordsOXYGEN BINDING / heme binding / truncated hemoglobin / nitrite reduction / pentacoordination
Function / homology
Function and homology information


thioredoxin peroxidase activity / cell redox homeostasis / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
: / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsHuwald, D. / Gasper, R. / Hemschemeier, A. / Hofmann, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationHE 5790/3-1 Germany
German Research FoundationRTG 2341 Germany
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions.
Authors: Huwald, D. / Duda, S. / Gasper, R. / Olieric, V. / Hofmann, E. / Hemschemeier, A.
History
DepositionNov 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5083
Polymers15,8651
Non-polymers6432
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-25 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.040, 42.620, 90.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein THB11


Mass: 15865.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_16g662750v5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K3CTN8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein 19 mg*ml-1 in 15 mM Tris-HCl pH 8.0 mixed 1:1 with 0.1 M HEPES pH 7.0, 21% PEG 6.000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.739 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 1.75→38.54 Å / Num. all: 594012 / Num. obs: 11933 / % possible obs: 94.26 % / Redundancy: 49.8 % / Biso Wilson estimate: 17.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09463 / Rpim(I) all: 0.01261 / Rrim(I) all: 0.09552 / Net I/σ(I): 38.39
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.5662 / Mean I/σ(I) obs: 2.64 / Num. unique all: 4429 / Num. unique obs: 711 / CC1/2: 0.83 / Rpim(I) all: 0.2366 / Rrim(I) all: 0.6174 / % possible all: 58.37

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PHASER2.7.18phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→38.54 Å / SU ML: 0.1825 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 19.6183
RfactorNum. reflection% reflection
Rfree0.2097 1194 10.01 %
Rwork0.1732 --
obs-11933 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.79 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 45 153 1216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481145
X-RAY DIFFRACTIONf_angle_d0.89281566
X-RAY DIFFRACTIONf_chiral_restr0.0407156
X-RAY DIFFRACTIONf_plane_restr0.0042200
X-RAY DIFFRACTIONf_dihedral_angle_d15.7041682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.3022810.2273734X-RAY DIFFRACTION59.36
1.82-1.90.26241240.19721103X-RAY DIFFRACTION90.15
1.9-20.21551350.1881216X-RAY DIFFRACTION98.54
2-2.130.2191380.16061247X-RAY DIFFRACTION99.35
2.13-2.290.20111390.16211247X-RAY DIFFRACTION100
2.29-2.520.24311400.16781270X-RAY DIFFRACTION99.93
2.52-2.890.19991420.18151267X-RAY DIFFRACTION99.93
2.89-3.640.19741420.1661283X-RAY DIFFRACTION100
3.64-45.130.1971530.17061372X-RAY DIFFRACTION99.93

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